This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Fragile Dreams: Farewell Ruins of the Moon
Once they find the exit from the underground mall, Personal Frame's occupational limit has been reached and her battery depletes. However, she has enough time to thank Seto for being her friend and saving her from a lonely death. Afterwards, Seto hugs her, tells her his name and then proceeds to bury her.
Many of the memory items are truly heartbreaking. Even more so after The Reveal.
In the class photo memory, the speaker notes that he had a very good life filled with little hardship. However, as he nears death, the realization hits him that he has no one to share this life with. The last line really pummels this anguish in: "... I'm scared."
In an interview with the director, producer, writer and designer Kawashima Kentarou he states that the glass cage project gave humans the ability to empathize without the use of words and they died when they used this power. So the survivors of the world are people who have never used this ability and thus, were truly alone in the world.
Everything about Crow's "death"...Just like PF, he begins speaking in monotone and repeating himself like a broken doll, before becoming coherent just for enough time to give a heartfelt goodbye to Seto.
The reveal before his death can also lead to to the realization that the humanoid robots you fight shortly afterword are the same model he was since they all have his voice as their dying screams. This can make it sound as if you keep hearing Crow dieEVERY time you kill one of them, which you may end up doing A LOT.
The creepy Chicken Merchant's love for his dead child "princess"...Just the fact that he probably reached Heroic BSOD and deluded himself into becoming the silly, naive collector of junk long ago and never recovered.